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If its a flat roof the it should be ok, it shouldnt be noisy if installed properly with noise reduction in mind, I like package units actually because they are less noisy, you dont have any equipment in the house to make noise.

If I were to install I would size and acoustically insulate duct properly, probably oversize a tad on the duct. I would also take as many measures as possible to eliminate vibration that could occur.

Crane rental is nothing to worry about, your contractor will have a crane in and out in 30 minutes and it doesnt cost a fortune.

And for the large hole in roof, Who cares? It will only be as large as the ducts under the roof curb, and everything will be sealed good as new by your hvac or roof contractor.